Creating a Heatmap

To generate a heatmap you need to select a group of samples you want to compare. Since we’ll be using samples from an existing project, we’ll need to first navigate to that project. Select Public in the right-hand corner of the header bar. This will take you to the list of public projects you can explore.

In the search box in the top left, search for Feline Gingivostomatitis.

Click on the Feline Gingivostomatitis project to navigate to the project folder. You can select a group of samples by checking the box to the left of each sample name. If you want to select all samples in a project, click the checkbox in the upper left corner (1). The number of selected samples will be visible on the top right of the table (2). After selecting at least two samples, click the Heatmap icon (3).

After clicking the Heatmap icon, you should see two options: Taxon Heatmap and AMR Heatmap (Deprecated). These are the two types of heatmaps that you can generate in CZ ID. Both let you see summary statistics about groups of samples and can be useful in multi-sample analysis. We are first going to walk through the features of the Taxon Heatmap.

Click on Taxon Heatmap from the dropdown menu. You will then be taken to the heatmap page.

Taxon Heatmap

When generating a taxon heatmap, CZ ID by default displays the 10 species with the highest reads per million for each sample. You can adjust the number of taxa per sample that are included in the heatmap using the available heatmap filters (see below). Because creating a heatmap pulls in a lot of data, it can sometimes take a few seconds to load when you first create it.

Add Taxon Button

While the heatmap is a great tool for surfacing the most abundant pathogens in your samples,

this may not include everything that you are interested in. Particularly when looking for

divergent viruses, it can be important to be able to add low abundance taxa to your heatmap.

You can add any taxon that was found in at least one of your samples by using the “Add taxon” button in the upper left corner of the heatmap.